Frequentist Inference for Thermal Load Sensitivity Models

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Documentation for package ‘freqTLS’ version 0.1.0

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aphid_tdt Cereal-aphid lethal-TDT data, three species across three ages
beta_binomial_tls Response families for thermal-load-sensitivity models
beta_tls Response families for thermal-load-sensitivity models
binomial_tls Response families for thermal-load-sensitivity models
check_tls Report identifiability diagnostics for a fitted model
clock_to_minutes Convert various clock formats to minutes
confint.profile_tls Confidence intervals for a fitted thermal-load-sensitivity model
derive_ctmax Derive the temperature giving a target survival at a fixed exposure
derive_lt Derive the lethal / survival-threshold duration at a temperature
derive_tcrit Derive the critical temperature at a damage-rate floor (T_crit)
diagnose_tdt_fit Diagnose a freqTLS fit (frequentist twin of 'diagnose_tdt_fit')
dsuzukii Drosophila suzukii multi-trait thermal-tolerance data
extract_tdt Extract z, CTmax and (optionally) T_crit with bootstrap confidence intervals
fit_4pl Fit the 4PL thermal-load-sensitivity model by maximum likelihood (TMB)
fit_tls Fit a single-stage 4PL thermal-load-sensitivity model by maximum likelihood
format_interval Format a point estimate plus confidence interval as a single string
get_ctmax Extract the CTmax estimate(s)
get_ctmax_draws Accessors for an extract_tdt() result
get_ctmax_summary Accessors for an extract_tdt() result
get_shape Extract the shape parameters (low, up, k, and phi)
get_tcrit_draws Accessors for an extract_tdt() result
get_tcrit_summary Accessors for an extract_tdt() result
get_z Extract the thermal-sensitivity (z) estimate(s)
get_z_draws Accessors for an extract_tdt() result
get_z_summary Accessors for an extract_tdt() result
heat_injury_envelope Parametric-bootstrap confidence envelope for a heat-injury trajectory
make_4pl_formula Build a freqTLS 4PL formula from the direct CTmax/z interface
plot.profile_tls_profile Plot a profile-likelihood deviance curve
plot_confidence_eye Confidence-Eye (or line) display of headline confidence intervals
plot_heat_injury Plot a heat-injury survival trajectory with a bootstrap confidence band
plot_survival_curves Plot fitted survival curves against duration
plot_survival_surface Plot the fitted survival surface over temperature and duration
plot_tdt_curve Plot the thermal death-time (TDT) curve: survival-threshold time vs temperature
predict.profile_tls Predict survival, link, or midpoint from a fitted freqTLS model
predict_heat_injury Predict cumulative heat injury under a temperature trace
predict_survival_curves Predict the fitted survival surface with bootstrap confidence bands
predict_survival_surface Predict a survival surface over a temperature-by-duration grid
print.profile_tls_profile Profile-likelihood curves for a fitted thermal-load-sensitivity model
profile.profile_tls Profile-likelihood curves for a fitted thermal-load-sensitivity model
ranef Random-effect BLUPs (conditional modes) for a freqTLS fit
ranef.profile_tls Random-effect BLUPs (conditional modes) for a freqTLS fit
shrimp_lethal Brown shrimp lethal thermal-death-time data
shrimp_sublethal Brown shrimp sublethal time-to-knockdown data
simulate_tls Simulate survival-count data from the 4PL thermal-load-sensitivity model
standardize_data Standardise a raw survival / proportion dataset for the TDT function library
tdt-accessors Accessors for an extract_tdt() result
tdt_parameter_table 4PL parameter table (frequentist twin of 'tdt_parameter_table')
tdt_quantile Quantile wrapper with TDT-friendly defaults
tidy_parameters Tidy the parameters of a fitted freqTLS model
tls Thermal-load-sensitivity quantities (z, CTmax) with confidence intervals
tls_bf Build a freqTLS formula object (brms/drmTMB-style)
tls_ctmax Thermal-load-sensitivity quantities (z, CTmax) with confidence intervals
tls_family Response families for thermal-load-sensitivity models
tls_tcrit Thermal-load-sensitivity quantities (z, CTmax) with confidence intervals
tls_z Thermal-load-sensitivity quantities (z, CTmax) with confidence intervals
ts_ci Uncertainty for the classical two-stage TDT quantities
ts_curve Median LT-vs-temperature line from a two-stage fit
ts_stage1 Stage 1 of the classical two-stage TDT pipeline
ts_stage2 Stage 2 of the classical two-stage TDT pipeline
zebrafish_lethal Zebrafish lethal thermal-death-time data across life stages
zebrafish_o2 Zebrafish lethal-TDT data across an oxygen gradient